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Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites.

Boucher MJ, Ghosh S, Zhang L, Lal A, Jang SW, Ju A, Zhang S, Wang X, Ralph SA, Zou J, Elias JE, Yeh E.

PLoS Biol. 2018 Sep 13;16(9):e2005895. doi: 10.1371/journal.pbio.2005895. [Epub ahead of print]


Developmental phosphoproteomics identifies the kinase CK2 as a driver of Hedgehog signaling and a therapeutic target in medulloblastoma.

Purzner T, Purzner J, Buckstaff T, Cozza G, Gholamin S, Rusert JM, Hartl TA, Sanders J, Conley N, Ge X, Langan M, Ramaswamy V, Ellis L, Litzenburger U, Bolin S, Theruvath J, Nitta R, Qi L, Li XN, Li G, Taylor MD, Wechsler-Reya RJ, Pinna LA, Cho YJ, Fuller MT, Elias JE, Scott MP.

Sci Signal. 2018 Sep 11;11(547). pii: eaau5147. doi: 10.1126/scisignal.aau5147.


Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors.

Pataki CI, Rodrigues J, Zhang L, Qian J, Efron B, Hastie T, Elias JE, Levitt M, Kopito RR.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8172-E8180. doi: 10.1073/pnas.1807981115. Epub 2018 Aug 13.


Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.

Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS, Huang KC, Sonnenburg JL.

Cell. 2018 Jun 14;173(7):1742-1754.e17. doi: 10.1016/j.cell.2018.05.008.


Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).

Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M.

Proteomics. 2018 Jun;18(12):e1800110. doi: 10.1002/pmic.201800110.


Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics.

Yang AC, du Bois H, Olsson N, Gate D, Lehallier B, Berdnik D, Brewer KD, Bertozzi CR, Elias JE, Wyss-Coray T.

J Am Chem Soc. 2018 Jun 13;140(23):7046-7051. doi: 10.1021/jacs.8b03074. Epub 2018 May 30.


T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins.

Olsson N, Schultz LM, Zhang L, Khodadoust MS, Narayan R, Czerwinski DK, Levy R, Elias JE.

Proteomics. 2018 Jun;18(12):e1700410. doi: 10.1002/pmic.201700410. Epub 2018 Apr 18.


Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD.

Proteomes. 2018 Jan 31;6(1). pii: E7. doi: 10.3390/proteomes6010007.


Liver transplantation in adults with liver disease due to common variable immunodeficiency leads to early recurrent disease and poor outcome.

Azzu V, Elias JE, Duckworth A, Davies S, Brais R, Kumararatne DS, Gimson AES, Griffiths WJH.

Liver Transpl. 2018 Feb;24(2):171-181. doi: 10.1002/lt.24979.


Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania.

Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL.

Science. 2017 Aug 25;357(6353):802-806. doi: 10.1126/science.aan4834.


RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation.

Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O.

J Biol Chem. 2017 Aug 11;292(32):13381-13390. doi: 10.1074/jbc.M117.784371. Epub 2017 Jun 27.


Characterization of protein complexes of the endoplasmic reticulum-associated degradation E3 ubiquitin ligase Hrd1.

Hwang J, Walczak CP, Shaler TA, Olzmann JA, Zhang L, Elias JE, Kopito RR.

J Biol Chem. 2017 Jun 2;292(22):9104-9116. doi: 10.1074/jbc.M117.785055. Epub 2017 Apr 14.


From mystery to mechanism: can proteomics build systems-level understanding of our gut microbes?

Gonzalez CG, Zhang L, Elias JE.

Expert Rev Proteomics. 2017 Jun;14(6):473-476. doi: 10.1080/14789450.2017.1311211. Epub 2017 Apr 3. No abstract available.


Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens.

Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, Czerwinski DK, Carlton VE, Moorhead M, Faham M, Kohrt HE, Carette J, Green MR, Davis MM, Levy R, Elias JE, Alizadeh AA.

Nature. 2017 Mar 30;543(7647):723-727. doi: 10.1038/nature21433. Epub 2017 Mar 22.


Relative Protein Quantification Using Tandem Mass Tag Mass Spectrometry.

Zhang L, Elias JE.

Methods Mol Biol. 2017;1550:185-198. doi: 10.1007/978-1-4939-6747-6_14.


The Prenylated Proteome of Plasmodium falciparum Reveals Pathogen-specific Prenylation Activity and Drug Mechanism-of-action.

Gisselberg JE, Zhang L, Elias JE, Yeh E.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S54-S64. doi: 10.1074/mcp.M116.064550. Epub 2016 Dec 31.


Building proteomic tool boxes to monitor MHC class I and class II peptides.

Schumacher FR, Delamarre L, Jhunjhunwala S, Modrusan Z, Phung QT, Elias JE, Lill JR.

Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600061. Review.


Meta-analyses and randomized trials investigating percutaneous coronary intervention of chronic total occlusions: what is left to explore?

Claessen BE, Hoebers LP, Elias JE, van Dongen IM, Henriques JP.

J Thorac Dis. 2016 Sep;8(9):E1100-E1102. No abstract available.


Erratum to: 'Pre-endoscopy point of care test (Simtomax- IgA/IgG-Deamidated Gliadin Peptide) for coeliac disease in iron deficiency anaemia: diagnostic accuracy and a cost saving economic model'.

Lau MS, Mooney PD, White WL, Appleby V, Moreea S, Haythem I, Elias JE, Bundhoo K, Corbett GD, Wong L, Tsai HH, Cross SS, Hebden JM, Hoque S, Sanders DS.

BMC Gastroenterol. 2016 Oct 5;16(1):122. No abstract available.


Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars.

Woo CM, Felix A, Zhang L, Elias JE, Bertozzi CR.

Anal Bioanal Chem. 2017 Jan;409(2):579-588. doi: 10.1007/s00216-016-9934-9. Epub 2016 Sep 30.


Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.

Lund PJ, Elias JE, Davis MM.

J Immunol. 2016 Oct 15;197(8):3086-3098. Epub 2016 Sep 21.


A pumpless microfluidic device driven by surface tension for pancreatic islet analysis.

Xing Y, Nourmohammadzadeh M, Elias JE, Chan M, Chen Z, McGarrigle JJ, Oberholzer J, Wang Y.

Biomed Microdevices. 2016 Oct;18(5):80. doi: 10.1007/s10544-016-0109-4.


Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens.

Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE.

Nature. 2016 Jul 7;535(7610):159-63. Epub 2016 Jun 17.


A PWWP Domain of Histone-Lysine N-Methyltransferase NSD2 Binds to Dimethylated Lys-36 of Histone H3 and Regulates NSD2 Function at Chromatin.

Sankaran SM, Wilkinson AW, Elias JE, Gozani O.

J Biol Chem. 2016 Apr 15;291(16):8465-74. doi: 10.1074/jbc.M116.720748. Epub 2016 Feb 24.


Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases.

Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE.

Cell Rep. 2016 Feb 9;14(5):1049-1061. doi: 10.1016/j.celrep.2016.01.009. Epub 2016 Jan 28.


Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.

Devabhaktuni A, Elias JE.

J Proteome Res. 2016 Mar 4;15(3):732-42. doi: 10.1021/acs.jproteome.5b00861. Epub 2016 Jan 25.


Reproductive Aging Drives Protein Accumulation in the Uterus and Limits Lifespan in C. elegans.

Zimmerman SM, Hinkson IV, Elias JE, Kim SK.

PLoS Genet. 2015 Dec 11;11(12):e1005725. doi: 10.1371/journal.pgen.1005725. eCollection 2015 Dec.


The effect of microbial colonization on the host proteome varies by gastrointestinal location.

Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE.

ISME J. 2016 May;10(5):1170-81. doi: 10.1038/ismej.2015.187. Epub 2015 Nov 17.


Quantitative Imaging of Gut Microbiota Spatial Organization.

Earle KA, Billings G, Sigal M, Lichtman JS, Hansson GC, Elias JE, Amieva MR, Huang KC, Sonnenburg JL.

Cell Host Microbe. 2015 Oct 14;18(4):478-88. doi: 10.1016/j.chom.2015.09.002. Epub 2015 Oct 1.


Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant's GI.

Elias JE.

Proteomics. 2015 Oct;15(20):3407-8. doi: 10.1002/pmic.201500359.


Monitoring host responses to the gut microbiota.

Lichtman JS, Sonnenburg JL, Elias JE.

ISME J. 2015 Sep;9(9):1908-15. doi: 10.1038/ismej.2015.93. Epub 2015 Jun 9. Review.


A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme.

Carlson SM, Moore KE, Sankaran SM, Reynoird N, Elias JE, Gozani O.

J Biol Chem. 2015 May 8;290(19):12040-7. doi: 10.1074/jbc.M115.641530. Epub 2015 Mar 20.


Idiopathic Non-Cirrhotic Intrahepatic Portal Hypertension (NCIPH)-Newer Insights into Pathogenesis and Emerging Newer Treatment Options.

Goel A, Elias JE, Eapen CE, Ramakrishna B, Elias E.

J Clin Exp Hepatol. 2014 Sep;4(3):247-56. doi: 10.1016/j.jceh.2014.07.005. Epub 2014 Jul 28. Review.


Calcineurin regulates the yeast synaptojanin Inp53/Sjl3 during membrane stress.

Guiney EL, Goldman AR, Elias JE, Cyert MS.

Mol Biol Cell. 2015 Feb 15;26(4):769-85. doi: 10.1091/mbc.E14-05-1019. Epub 2014 Dec 17.


The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis.

Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P.

Cell Cycle. 2014;13(18):2889-900. doi: 10.4161/15384101.2014.946850.


Role of disease-associated tolerance in infectious superspreaders.

Gopinath S, Lichtman JS, Bouley DM, Elias JE, Monack DM.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15780-5. doi: 10.1073/pnas.1409968111. Epub 2014 Oct 20.


The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis.

Treeck M, Sanders JL, Gaji RY, LaFavers KA, Child MA, Arrizabalaga G, Elias JE, Boothroyd JC.

PLoS Pathog. 2014 Jun 19;10(6):e1004197. doi: 10.1371/journal.ppat.1004197. eCollection 2014 Jun.


Assessing subunit dependency of the Plasmodium proteasome using small molecule inhibitors and active site probes.

Li H, van der Linden WA, Verdoes M, Florea BI, McAllister FE, Govindaswamy K, Elias JE, Bhanot P, Overkleeft HS, Bogyo M.

ACS Chem Biol. 2014 Aug 15;9(8):1869-76. doi: 10.1021/cb5001263. Epub 2014 Jun 19.


Host-centric proteomics of stool: a novel strategy focused on intestinal responses to the gut microbiota.

Lichtman JS, Marcobal A, Sonnenburg JL, Elias JE.

Mol Cell Proteomics. 2013 Nov;12(11):3310-8. doi: 10.1074/mcp.M113.029967. Epub 2013 Aug 27.


A role for the MRN complex in ATR activation via TOPBP1 recruitment.

Duursma AM, Driscoll R, Elias JE, Cimprich KA.

Mol Cell. 2013 Apr 11;50(1):116-22. doi: 10.1016/j.molcel.2013.03.006.


Prognostic significance of von willebrand factor in cirrhosis: a possible mechanism.

Eapen CE, Elias JE, Mackie I, Elias E.

Hepatology. 2013 Sep;58(3):1189. doi: 10.1002/hep.26282. Epub 2013 Jul 29. No abstract available.


Porto-pulmonary hypertension exacerbated by platelet transfusion in a patient with ADAMTS13 deficiency.

Elias JE, Mackie I, Eapen CE, Chu P, Shaw JC, Elias E.

J Hepatol. 2013 Apr;58(4):827-30. doi: 10.1016/j.jhep.2012.11.003. Epub 2012 Nov 10.


The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries.

Treeck M, Sanders JL, Elias JE, Boothroyd JC.

Cell Host Microbe. 2011 Oct 20;10(4):410-9. doi: 10.1016/j.chom.2011.09.004.


A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers.

Jirawatnotai S, Hu Y, Michowski W, Elias JE, Becks L, Bienvenu F, Zagozdzon A, Goswami T, Wang YE, Clark AB, Kunkel TA, van Harn T, Xia B, Correll M, Quackenbush J, Livingston DM, Gygi SP, Sicinski P.

Nature. 2011 Jun 8;474(7350):230-4. doi: 10.1038/nature10155.


The dynamic state of protein turnover: It's about time.

Hinkson IV, Elias JE.

Trends Cell Biol. 2011 May;21(5):293-303. doi: 10.1016/j.tcb.2011.02.002. Epub 2011 Apr 7. Review.


Synthetic small interfering RNA down-regulates caspase-3 and affects apoptosis, IL-1 β, and viability of porcine proximal tubular cells.

Yang B, Elias JE, Bloxham M, Nicholson ML.

J Cell Biochem. 2011 May;112(5):1337-47. doi: 10.1002/jcb.23050.


A tissue-specific atlas of mouse protein phosphorylation and expression.

Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP.

Cell. 2010 Dec 23;143(7):1174-89. doi: 10.1016/j.cell.2010.12.001.


The role of students as teachers: four years' experience of a large-scale, peer-led programme.

Batchelder AJ, Rodrigues CM, Lin LY, Hickey PM, Johnson C, Elias JE.

Med Teach. 2010;32(7):547-51. doi: 10.3109/0142159X.2010.490861.


Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.

Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P.

Nature. 2010 Jan 21;463(7279):374-8. doi: 10.1038/nature08684.


Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

Hemming ML, Elias JE, Gygi SP, Selkoe DJ.

PLoS One. 2009 Dec 29;4(12):e8477. doi: 10.1371/journal.pone.0008477.

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